SNPit: a federated data integration system for the purpose of functional SNP annotation.

Publication Type:

Journal Article

Source:

Computer methods and programs in biomedicine, Volume 95, Issue 2, p.181-9 (2009)

Keywords:

2009, Center-Authored Paper, Chromosome Mapping, Database Management Systems, Databases, Genetic, DNA Mutational Analysis, Documentation, Information Storage and Retrieval, Internet, Polymorphism, Single Nucleotide, Public Health Sciences Division, Software, Systems Integration

Abstract:

Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was included through an inference engine plug in. The SNPit web servlet is available online for use. SNPit allows users to go to one source for up-to-date information on the functional annotation of SNPs. A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies.